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You can use webdav to upload your input files today. If you put it in a subdirectory of the opensees2 directory (in your hub HOME directory) then you will see an option to execute this input file from this tool (opensees2). For example, create a directory called
/home/neeshub//opensees2/mysim

Then place your tcl file with its input files in
/home/neeshub//opensees2/mysim/mysim.tcl

When you do this, mysim will be an option in the opensees2 tool. You can put the inputs to mysim.tcl in the same directory. You will notice that the directory opensees2 already has some other subdirectories set up as examples.